I've come across this in v7 when you attempt to access images or other items in the App_Themes directory. I'm wondering if it has to do with the URL rewrite process.
You might also register all your stylesheets in the the Site Manager>Development>Css Stylesheets section and loading them in your master page header like below vs. letting the asp.net engine load them automatically:
<link rel="stylesheet" href="/CMSPages/GetResource.ashx?stylesheetfile=/App_Themes/StandardProcess/styles/main.css" type="text/css" />
This is using the standard handler to get and process the stylesheet then. This has changed from v6 to v7 if I remember right. Also by registering them in the UI, I believe they will automatically be processed like above (using the getresource.ashx handler) so no need to worry about the other problems.